Plant Detection in RGB Images from Unmanned Aerial Vehicles Using Segmentation by Deep Learning and an Impact of Model Accuracy on Downstream Analysis.

Crop field monitoring using unmanned aerial vehicles (UAVs) is one of the most important technologies for plant growth control in modern precision agriculture. One of the important and widely used tasks in field monitoring is plant stand counting. The accurate identification of plants in field images provides estimates of plant number per unit area, detects missing seedlings, and predicts crop yield.

A pipeline for processing hyperspectral images, with a case of melanin-containing barley grains as an example.

Analysis of hyperspectral images is of great interest in plant studies. Nowadays, this analysis is used more and more widely, so the development of hyperspectral image processing methods is an urgent task. This paper presents a hyperspectral image processing pipeline that includes: preprocessing, basic statistical analysis, visualization of a multichannel hyperspectral image, and solving classification and clustering problems using machine learning methods.

Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in L.

The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing.

Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods.

The pigment composition of plant seed coat affects important properties such as resistance to pathogens, pre-harvest sprouting, and mechanical hardness. The dark color of barley (Hordeum vulgare L.) grain can be attributed to the synthesis and accumulation of two groups of pigments.

Image-based classification of wheat spikes by glume pubescence using convolutional neural networks.

Introduction: Pubescence is an important phenotypic trait observed in both vegetative and generative plant organs. Pubescent plants demonstrate increased resistance to various environmental stresses such as drought, low temperatures, and pests. It serves as a significant morphological marker and aids in selecting stress-resistant cultivars, particularly in wheat.

GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing.

The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations.

ICAnnoLncRNA: A Snakemake Pipeline for a Long Non-Coding-RNA Search and Annotation in Transcriptomic Sequences.

Long non-coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not encode proteins. Experimental studies have shown the diversity and importance of lncRNA functions in plants. To expand knowledge about lncRNAs in other species, computational pipelines that allow for standardised data-processing steps in a mode that does not require user control up until the final result were actively developed recently.

[Molecular Mechanisms to Optimize Gene Translation Elongation Differ Significantly in Bacteria with and without Nonribosomal Peptides].

Nonribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes that form gene clusters in bacterial genomes.

Human phospholipases A2: a functional and evolutionary analysis.

Phospholipases A2 (PLA2) are capable of hydrolyzing the sn-2 position of glycerophospholipids to release fatty acids and lysophospholipids. The PLA2 superfamily enzymes are widespread and present in most mammalian cells and tissues, regulating metabolism, remodeling the membrane and maintaining its homeostasis, producing lipid mediators and activating inflammatory reactions, so disruption of PLA2-regulated lipid metabolism often leads to various diseases. In this study, 29 PLA2 genes in the human genome were systematically collected and described based on literature and sequence analyses.

QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing.

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season.

Relationship between the Characteristics of Bread Wheat Grains, Storage Time and Germination.

Seed storage is important to farmers, breeders and for germplasm preservation. During storage, seeds accumulate damage at the structural and metabolic level, which disrupt their function and reduce resistance to adverse external conditions. In this regard, issues related to seed aging prove to be relevant for maintaining the viability of genetic collections.

Potato spindle tuber viroid.

Viroids belong to a very interesting class of molecules attracting researchers in phytopathology and molecular evolution. Here we review recent literature data concerning the genetics of Potato spindle tuber viroid (PSTVd) and the mechanisms related to its pathological effect on the host plants. PSTVd can be transmitted vertically through microspores and macrospores, but not with pollen from another infected plant.

[Ribosomal profiling as a tool for studying translation in plants: main results, problems and future prospects].

The expression of eukaryotic genes can be regulated at several stages, including the translation of mRNA. It is known that the structure of mRNA can affect both the efficiency of interaction with the translation apparatus in general and the choice of translation initiation sites. To study the translated fraction of the transcriptome, experimental methods of analysis were developed, the most informative of which is ribosomal profiling (RP, Ribo-seq).

Determination of the quantitative content of chlorophylls in leaves by reflection spectra using the random forest algorithm.

Determining the quantitative content of chlorophylls in plant leaves by their reflection spectra is an important task both in monitoring the state of natural and industrial phytocenoses, and in laboratory studies of normal and pathological processes during plant growth. The use of machine learning methods for these purposes is promising, since these methods allow inferring the relationships between input and output variables (prediction model), and in order to improve the quality of the prediction, a researcher may modify predictors and selects a set of method parameters. Here, we present the results of the implementation and evaluation of the random forest algorithm for predicting the total concentration of chlorophylls a and b from the reflection spectra of plant leaves in the visible and infrared wavelengths.

Image-Based Wheat Fungi Diseases Identification by Deep Learning.

Diseases of cereals caused by pathogenic fungi can significantly reduce crop yields. Many cultures are exposed to them. The disease is difficult to control on a large scale; thus, one of the relevant approaches is the crop field monitoring, which helps to identify the disease at an early stage and take measures to prevent its spread.

Analysis of color and texture characteristics of cereals on digital images.

The color of the grain shell of cereals is an important feature that characterizes the pigments and metabolites contained in it. The grain shell is the main barrier between the grain and the environment, so its characteristics are associated with a number of important biological functions: moisture absorption, grain viability, resistance to pre-harvest germination. The presence of pigments in the shell affects various technological properties of the grain.

Quantifying adults with the use of a smartphone.

A method for automation of imago quantifying and fecundity assessment in with the use of mobile devices running Android operating system is proposed. The traditional manual method of counting the progeny takes a long time and limits the opportunity of making large-scale experiments. Thus, the development of computerized methods that would allow us to automatically make a quantitative estimate of fecundity is an urgent requirement.

The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family.

YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene transfer (HGT) from bacteria to the most recent common ancestor (MRCA) of land plants or to have inherited it from their ancestor, the charophyte algae. To refine YUCCA origin, we performed a phylogenetic analysis of the class B flavoprotein monooxygenases and comparative analysis of the sequences belonging to different families of this protein class.

Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain.

Antimicrobial peptides (AMPs) are natural antagonistic tools of many bacteria and are considered as attractive antimicrobial agents for the treatment of bacteria with multidrug resistance. Lactic acid bacteria from the gastrointestinal tract of animals and human produce various AMPs inhibiting the growth of pathogens. Here we report the isolation and identification of novel Lactobacillus fermentum strain HF-D1 from the human gut producing AMPs which prevents the growth of P.

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in .

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution.

Web-Based Computational Tools for the Prediction and Analysis of Posttranslational Modifications of Proteins.

The increase in the number of Web-based resources on posttranslational modification sites (PTMSs) in proteins is accelerating. This chapter presents a set of computational protocols describing how to work with the Internet resources when dealing with PTMSs. The protocols are intended for querying in PTMS-related databases, search of the PTMSs in the protein sequences and structures, and calculating the pI and molecular mass of the PTM isoforms.

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes.

Background: The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in their definitive hosts, although their populations have substantially different ecogeographical aspects including habitat, preferred hosts, population structure. Lack of O.